Update optimizeBlackDots following experience using it during May 2022 run

During May 2022 run and previous conversations, I noticed few things in how the algorithm could be improved:

1. Implement random seed, so that runs create a same solution
2. there are several spurious lines that duplicate plotting commands and which can be removed (noticed by hassan)
3. make the input data accessible outside of the black dot optimization class

These are all relatively minor quality-of-life improvements.